Alpha-diversity

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See the documentation of the MiscMetabar package for example of alpha diversity analysis.

if(base::interactive()) {
  params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interest

library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/02_alpha_diversity.qmd")
source(here::here("R/styles.R"))

d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))

Cleaning suppress 3 taxa and 13 samples.

hill_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, one_plot = TRUE) &
  (
    theme_idest(
      subtitle_size = 8,
      plot_title_size = 12,
      plot_margin = margin(5, 10, 5, 10),
      axis_title_size = 9,
      axis_text_size = 8
    ) + theme(legend.position = "none")
  ) 

Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable

MiscMetabar::accu_plot_balanced_modality(d_pq, factor_of_interest, nperm=20) + theme_idest()

`set.seed(1)` was used to initialize repeatable random subsampling.

Please record this for your records so others can reproduce.

Try `set.seed(1); .Random.seed` for the full vector

...

Error in validObject(.Object): objet de classe "sample_data" incorrect: Sample Data must have non-zero dimensions.

ggbetween_pq(d_pq, factor_of_interest)

Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'object' lors de la s�lection d'une m�thode pour la fonction 'sample_data' : colonnes non définies sélectionnées

Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt .

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] MiscMetabar_0.10.1 purrr_1.0.2        dplyr_1.1.4        dada2_1.34.0      
[5] Rcpp_1.0.13-1      ggplot2_3.5.1      phyloseq_1.50.0    targets_1.9.0     
[9] knitr_1.49        

loaded via a namespace (and not attached):
  [1] bitops_1.0-9                deldir_2.0-4               
  [3] permute_0.9-7               rlang_1.1.4                
  [5] magrittr_2.0.3              ade4_1.7-22                
  [7] matrixStats_1.4.1           compiler_4.4.2             
  [9] mgcv_1.9-1                  png_0.1-8                  
 [11] callr_3.7.6                 vctrs_0.6.5                
 [13] reshape2_1.4.4              stringr_1.5.1              
 [15] pwalign_1.2.0               pkgconfig_2.0.3            
 [17] crayon_1.5.3                fastmap_1.2.0              
 [19] backports_1.5.0             XVector_0.46.0             
 [21] utf8_1.2.4                  Rsamtools_2.22.0           
 [23] rmarkdown_2.29              UCSC.utils_1.2.0           
 [25] ps_1.8.1                    xfun_0.49                  
 [27] zlibbioc_1.52.0             GenomeInfoDb_1.42.0        
 [29] jsonlite_1.8.9              biomformat_1.34.0          
 [31] rhdf5filters_1.18.0         DelayedArray_0.32.0        
 [33] Rhdf5lib_1.28.0             BiocParallel_1.40.0        
 [35] jpeg_0.1-10                 parallel_4.4.2             
 [37] cluster_2.1.6               R6_2.5.1                   
 [39] RColorBrewer_1.1-3          stringi_1.8.4              
 [41] GenomicRanges_1.58.0        SummarizedExperiment_1.36.0
 [43] iterators_1.0.14            IRanges_2.40.0             
 [45] Matrix_1.7-1                splines_4.4.2              
 [47] igraph_2.1.1                tidyselect_1.2.1           
 [49] abind_1.4-8                 yaml_2.3.10                
 [51] vegan_2.6-8                 codetools_0.2-20           
 [53] hwriter_1.3.2.1             processx_3.8.4             
 [55] lattice_0.22-6              tibble_3.2.1               
 [57] plyr_1.8.9                  Biobase_2.66.0             
 [59] withr_3.0.2                 ShortRead_1.64.0           
 [61] evaluate_1.0.1              survival_3.7-0             
 [63] RcppParallel_5.1.9          Biostrings_2.74.0          
 [65] pillar_1.9.0                BiocManager_1.30.25        
 [67] MatrixGenerics_1.18.0       renv_1.0.11                
 [69] foreach_1.5.2               stats4_4.4.2               
 [71] generics_0.1.3              rprojroot_2.0.4            
 [73] S4Vectors_0.44.0            munsell_0.5.1              
 [75] scales_1.3.0                base64url_1.4              
 [77] glue_1.8.0                  tools_4.4.2                
 [79] interp_1.1-6                data.table_1.16.2          
 [81] GenomicAlignments_1.42.0    rhdf5_2.50.0               
 [83] grid_4.4.2                  ape_5.8                    
 [85] latticeExtra_0.6-30         colorspace_2.1-1           
 [87] nlme_3.1-166                GenomeInfoDbData_1.2.13    
 [89] cli_3.6.3                   fansi_1.0.6                
 [91] S4Arrays_1.6.0              gtable_0.3.6               
 [93] digest_0.6.37               BiocGenerics_0.52.0        
 [95] SparseArray_1.6.0           htmlwidgets_1.6.4          
 [97] htmltools_0.5.8.1           multtest_2.62.0            
 [99] lifecycle_1.0.4             here_1.0.1                 
[101] httr_1.4.7                  secretbase_1.0.3           
[103] MASS_7.3-61